Custom LNA mRNA Detection Probes

For detecting short RNAs and discriminating highly similar RNAs by in situ hybridization with LNA-enhanced probes

Sensitivity and specificity superior to DNA probes and riboprobes

Online tools provide optimally designed LNA-enhanced probe in minutes

Available with a wide selection of labels

No cloning expertise required

Excellent tissue penetration

Custom design your own LNA-enhanced detection probes for any mRNA or lncRNA target in just minutes using our advanced online design tools. Custom LNA mRNA Detection Probes allow you to easily detect short RNAs and discriminate between highly similar RNAs. High affinity for their target sequences allows use of stringent hybridization and washing conditions, despite short probe lengths.

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The intensities of four probes
targeting rRNA from E. coli were compared. All probes had the same 19 nucleotide sequence, but the Custom LNA mRNA Detection Probes
had 1–3 LNA subsitutions. The LNA Probe 3 produced 22 times higher intensity than the DNA probe. Data from Kubota et al. Appl. Environ. Microbiol. 2006. 72: 5311–7.

Custom LNA mRNA Detection Probes can also be used to discriminate between different splicing variants, isoforms and to detect the trinucleotide repeats associated with some diseases.
In addition, the probes are great for detecting short non-coding RNAs and have been widely used for miRNA detection. In some cases, LNA Detection Probes give a signal intensity over 20 times higher than that from DNA probes (see figure Custom LNA mRNA Detection Probes give stronger signals than DNA probes).

Principle

Features

Custom LNA mRNA Detection Probes are great for detecting short RNAs and for discriminating between highly similar RNAs. The high affinity of these probes for their target sequences allows use of stringent hybridization and washing conditions, despite the short probe lengths. Our online design tool enables you to easily design highly sensitive LNA probes for your specific mRNA sequence.

Product description

Custom LNA mRNA Detection Probes are available with a large selection of 3' or 5' labels or in ready-to-label format for your own custom labeling. Double (5' and 3') DIG-labeled probes are the most sensitive detection probes available, due to the synergistic effect between the two labels. Therefore, we generally recommend this labeling option. The design tool allows you to choose between several different probe synthesis scales and modifiers.

Probe design process

Our online design tool uses a sophisticated algorithm to quickly identify optimal LNA-enhanced probes for your target mRNA. The tool quickly evaluates more than 5,000 probe designs based on over 20 design criteria. This process ensures that high-quality probes can be designed for any mRNA sequence. The design criteria include the following:

Optimization of probe length and the number and positions of LNA bases within the probe: ensures that the probes have the correct melting temperatures and avoids any potential self-hybridization.

A detailed analysis of the probe's LNA pattern, based on our extensive knowledge of oligonucleotide design rules: ensures that LNA bases are not placed in positions where they could negatively affect the performance of the probe.

Calculations of the target’s secondary structure: ensures that the probes only target accessible regions of the mRNA.

BLAST searches: ensure that the probes will only target the relevant mRNA sequence.

Applications

Custom LNA mRNA Detection Probes are great for in situ hybridization applications requiring a short probe, such as in the detection of short sequences or for discriminating between closely related sequences.